[2023-06-27 08:37:16,374] [INFO] DFAST_QC pipeline started.
[2023-06-27 08:37:16,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 08:37:16,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference
[2023-06-27 08:37:17,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 08:37:17,595] [INFO] Task started: Prodigal
[2023-06-27 08:37:17,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg788958d3-bace-439c-ab3d-b697c81288b5/GCA_002255495.1_ASM225549v1_genomic.fna.gz | prodigal -d GCA_002255495.1_ASM225549v1_genomic.fna/cds.fna -a GCA_002255495.1_ASM225549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 08:37:26,410] [INFO] Task succeeded: Prodigal
[2023-06-27 08:37:26,411] [INFO] Task started: HMMsearch
[2023-06-27 08:37:26,411] [INFO] Running command: hmmsearch --tblout GCA_002255495.1_ASM225549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/reference_markers.hmm GCA_002255495.1_ASM225549v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 08:37:26,712] [INFO] Task succeeded: HMMsearch
[2023-06-27 08:37:26,713] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg788958d3-bace-439c-ab3d-b697c81288b5/GCA_002255495.1_ASM225549v1_genomic.fna.gz]
[2023-06-27 08:37:26,742] [INFO] Query marker FASTA was written to GCA_002255495.1_ASM225549v1_genomic.fna/markers.fasta
[2023-06-27 08:37:26,743] [INFO] Task started: Blastn
[2023-06-27 08:37:26,743] [INFO] Running command: blastn -query GCA_002255495.1_ASM225549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/reference_markers.fasta -out GCA_002255495.1_ASM225549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:37:27,403] [INFO] Task succeeded: Blastn
[2023-06-27 08:37:27,406] [INFO] Selected 25 target genomes.
[2023-06-27 08:37:27,407] [INFO] Target genome list was writen to GCA_002255495.1_ASM225549v1_genomic.fna/target_genomes.txt
[2023-06-27 08:37:27,417] [INFO] Task started: fastANI
[2023-06-27 08:37:27,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg788958d3-bace-439c-ab3d-b697c81288b5/GCA_002255495.1_ASM225549v1_genomic.fna.gz --refList GCA_002255495.1_ASM225549v1_genomic.fna/target_genomes.txt --output GCA_002255495.1_ASM225549v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 08:37:43,469] [INFO] Task succeeded: fastANI
[2023-06-27 08:37:43,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 08:37:43,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 08:37:43,483] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 08:37:43,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 08:37:43,484] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.8992	186	914	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.8286	177	914	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.7291	224	914	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3173	135	914	95	below_threshold
Acidisoma cellulosilyticum	strain=HW T5.17	GCA_020621385.1	2802395	2802395	type	True	76.1085	120	914	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	75.9435	86	914	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.7107	132	914	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.6394	84	914	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.6241	105	914	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.6021	89	914	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	75.534	106	914	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	75.519	111	914	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.3962	83	914	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	75.385	100	914	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.3629	87	914	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	75.1133	50	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 08:37:43,486] [INFO] DFAST Taxonomy check result was written to GCA_002255495.1_ASM225549v1_genomic.fna/tc_result.tsv
[2023-06-27 08:37:43,486] [INFO] ===== Taxonomy check completed =====
[2023-06-27 08:37:43,486] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 08:37:43,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/checkm_data
[2023-06-27 08:37:43,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 08:37:43,519] [INFO] Task started: CheckM
[2023-06-27 08:37:43,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002255495.1_ASM225549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002255495.1_ASM225549v1_genomic.fna/checkm_input GCA_002255495.1_ASM225549v1_genomic.fna/checkm_result
[2023-06-27 08:38:15,272] [INFO] Task succeeded: CheckM
[2023-06-27 08:38:15,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 08:38:15,319] [INFO] ===== Completeness check finished =====
[2023-06-27 08:38:15,320] [INFO] ===== Start GTDB Search =====
[2023-06-27 08:38:15,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002255495.1_ASM225549v1_genomic.fna/markers.fasta)
[2023-06-27 08:38:15,321] [INFO] Task started: Blastn
[2023-06-27 08:38:15,321] [INFO] Running command: blastn -query GCA_002255495.1_ASM225549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d804eae-d5da-452c-b39b-4134d3c7f55b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002255495.1_ASM225549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:38:16,324] [INFO] Task succeeded: Blastn
[2023-06-27 08:38:16,328] [INFO] Selected 21 target genomes.
[2023-06-27 08:38:16,328] [INFO] Target genome list was writen to GCA_002255495.1_ASM225549v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 08:38:16,336] [INFO] Task started: fastANI
[2023-06-27 08:38:16,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg788958d3-bace-439c-ab3d-b697c81288b5/GCA_002255495.1_ASM225549v1_genomic.fna.gz --refList GCA_002255495.1_ASM225549v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002255495.1_ASM225549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 08:38:31,830] [INFO] Task succeeded: fastANI
[2023-06-27 08:38:31,853] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 08:38:31,853] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002255495.1	s__20-60-12 sp002255495	100.0	901	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__20-60-12	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900156265.1	s__Acidiphilium rubrum	77.092	207	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	-
GCF_000202835.1	s__Acidiphilium multivorum	76.886	187	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_008630155.1	s__Rhodovastum atsumiense	76.3019	135	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255575.1	s__Acidocella sp002255575	76.2882	145	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.72	99.72	0.92	0.92	2	-
GCA_011332665.1	s__Acidibrevibacterium sp011332665	76.111	111	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241425.1	s__JAFAXA01 sp019241425	76.0693	80	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386565.1	s__Roseomonas oryzae	75.9256	87	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765975.1	s__Rhodopila sp009765975	75.908	102	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851415.1	s__Rhodopila sp903851415	75.9027	102	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.89	99.89	0.92	0.92	2	-
GCA_003133265.1	s__PALSA-911 sp003133265	75.7329	102	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	75.7007	133	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845065.1	s__CAIYPH01 sp903845065	75.6545	119	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101615.1	s__Belnapia rosea	75.5283	110	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCA_014376425.1	s__Rhodovarius sp014376425	75.2555	55	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896535.1	s__CAITYE01 sp903896535	75.2511	81	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAITYE01	95.0	99.30	99.07	0.87	0.85	4	-
GCA_016792765.1	s__SBBV01 sp016792765	75.1925	56	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164305.1	s__BOG-934 sp003164305	75.0822	50	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-934	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238725.1	s__Bin65 sp002238725	74.9291	50	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 08:38:31,873] [INFO] GTDB search result was written to GCA_002255495.1_ASM225549v1_genomic.fna/result_gtdb.tsv
[2023-06-27 08:38:31,875] [INFO] ===== GTDB Search completed =====
[2023-06-27 08:38:31,881] [INFO] DFAST_QC result json was written to GCA_002255495.1_ASM225549v1_genomic.fna/dqc_result.json
[2023-06-27 08:38:31,882] [INFO] DFAST_QC completed!
[2023-06-27 08:38:31,882] [INFO] Total running time: 0h1m16s